Multiple sequence alignment - TraesCS4A01G180500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G180500 chr4A 100.000 2687 0 0 1 2687 454764844 454762158 0.000000e+00 4963
1 TraesCS4A01G180500 chr4B 92.775 2173 97 25 176 2320 181005057 181007197 0.000000e+00 3088
2 TraesCS4A01G180500 chr4B 91.406 128 4 4 2412 2539 181007391 181007511 4.600000e-38 169
3 TraesCS4A01G180500 chr4B 90.816 98 4 2 2316 2413 181007268 181007360 2.810000e-25 126
4 TraesCS4A01G180500 chr4D 94.023 1874 70 23 466 2320 118575533 118577383 0.000000e+00 2802
5 TraesCS4A01G180500 chr4D 92.857 154 10 1 315 467 118574912 118575065 3.480000e-54 222
6 TraesCS4A01G180500 chr7B 91.787 414 19 2 1031 1444 6961752 6962150 1.810000e-156 562
7 TraesCS4A01G180500 chr7B 91.727 411 18 3 1034 1444 630506665 630507059 8.400000e-155 556
8 TraesCS4A01G180500 chr7B 90.676 429 23 5 1018 1444 745073015 745073428 3.020000e-154 555
9 TraesCS4A01G180500 chr6A 90.521 422 25 2 1023 1444 245231407 245231001 6.540000e-151 544
10 TraesCS4A01G180500 chr3A 90.284 422 17 3 1023 1444 628782002 628781605 5.090000e-147 531
11 TraesCS4A01G180500 chr3A 88.863 422 23 4 1023 1444 37898816 37898419 5.170000e-137 497
12 TraesCS4A01G180500 chr3A 88.152 422 26 3 1023 1444 149408381 149407984 5.200000e-132 481
13 TraesCS4A01G180500 chr5B 90.511 411 22 5 1034 1444 23308733 23308340 6.590000e-146 527
14 TraesCS4A01G180500 chr7A 88.811 429 22 4 1018 1444 458333926 458334330 1.110000e-138 503
15 TraesCS4A01G180500 chr3B 94.558 147 6 2 1300 1444 791023535 791023681 2.690000e-55 226
16 TraesCS4A01G180500 chr3B 90.506 158 11 4 1289 1444 791026710 791026555 3.510000e-49 206


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G180500 chr4A 454762158 454764844 2686 True 4963.000000 4963 100.000000 1 2687 1 chr4A.!!$R1 2686
1 TraesCS4A01G180500 chr4B 181005057 181007511 2454 False 1127.666667 3088 91.665667 176 2539 3 chr4B.!!$F1 2363
2 TraesCS4A01G180500 chr4D 118574912 118577383 2471 False 1512.000000 2802 93.440000 315 2320 2 chr4D.!!$F1 2005

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
217 218 0.035056 CCCGGAATCAAAGCTGTCCT 60.035 55.0 0.73 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 2228 1.981256 AAACGAATCAACCAGCCACT 58.019 45.0 0.0 0.0 0.0 4.0 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.717313 GAAGTGGCCACCGGGGTC 62.717 72.222 32.29 17.27 43.63 4.46
40 41 2.677971 GTCGGAATGACCATCGGTG 58.322 57.895 0.00 0.00 42.04 4.94
41 42 1.153449 TCGGAATGACCATCGGTGC 60.153 57.895 0.00 0.00 35.25 5.01
42 43 1.449423 CGGAATGACCATCGGTGCA 60.449 57.895 0.00 0.00 35.25 4.57
43 44 1.431488 CGGAATGACCATCGGTGCAG 61.431 60.000 0.00 0.00 35.25 4.41
44 45 1.718757 GGAATGACCATCGGTGCAGC 61.719 60.000 5.64 5.64 35.25 5.25
45 46 2.040213 GAATGACCATCGGTGCAGCG 62.040 60.000 31.22 31.22 35.25 5.18
46 47 2.520465 AATGACCATCGGTGCAGCGA 62.520 55.000 39.01 39.01 35.25 4.93
47 48 2.887568 GACCATCGGTGCAGCGAG 60.888 66.667 39.08 30.10 35.25 5.03
48 49 4.457496 ACCATCGGTGCAGCGAGG 62.457 66.667 39.08 38.18 32.98 4.63
85 86 2.434359 GAAGTGGCCTTCGACGGG 60.434 66.667 10.33 4.65 37.92 5.28
86 87 2.920912 AAGTGGCCTTCGACGGGA 60.921 61.111 10.33 0.00 0.00 5.14
87 88 2.837371 GAAGTGGCCTTCGACGGGAG 62.837 65.000 10.33 0.00 37.92 4.30
88 89 3.379445 GTGGCCTTCGACGGGAGA 61.379 66.667 10.33 0.00 0.00 3.71
89 90 3.068691 TGGCCTTCGACGGGAGAG 61.069 66.667 10.33 0.00 0.00 3.20
90 91 4.516195 GGCCTTCGACGGGAGAGC 62.516 72.222 10.33 0.00 0.00 4.09
91 92 4.856607 GCCTTCGACGGGAGAGCG 62.857 72.222 10.33 0.00 0.00 5.03
92 93 4.194720 CCTTCGACGGGAGAGCGG 62.195 72.222 0.00 0.00 33.51 5.52
93 94 4.194720 CTTCGACGGGAGAGCGGG 62.195 72.222 0.00 0.00 33.51 6.13
118 119 1.355043 GGGCTAGGCTAGGCTAGACTA 59.645 57.143 41.94 30.39 44.01 2.59
122 123 2.579410 AGGCTAGGCTAGACTAGAGC 57.421 55.000 32.97 22.51 44.01 4.09
123 124 1.161843 GGCTAGGCTAGACTAGAGCG 58.838 60.000 32.97 10.79 42.40 5.03
124 125 1.161843 GCTAGGCTAGACTAGAGCGG 58.838 60.000 32.97 10.42 42.40 5.52
125 126 1.543871 GCTAGGCTAGACTAGAGCGGT 60.544 57.143 32.97 0.00 42.40 5.68
126 127 2.147958 CTAGGCTAGACTAGAGCGGTG 58.852 57.143 26.25 0.00 42.40 4.94
127 128 1.104577 AGGCTAGACTAGAGCGGTGC 61.105 60.000 13.91 0.00 41.06 5.01
128 129 1.104577 GGCTAGACTAGAGCGGTGCT 61.105 60.000 13.91 0.00 43.88 4.40
129 130 1.595466 GCTAGACTAGAGCGGTGCTA 58.405 55.000 13.91 0.00 39.88 3.49
130 131 1.264826 GCTAGACTAGAGCGGTGCTAC 59.735 57.143 13.91 0.00 39.88 3.58
131 132 1.874872 CTAGACTAGAGCGGTGCTACC 59.125 57.143 3.13 0.00 39.88 3.18
132 133 0.256464 AGACTAGAGCGGTGCTACCT 59.744 55.000 0.00 0.00 39.88 3.08
133 134 1.489649 AGACTAGAGCGGTGCTACCTA 59.510 52.381 0.00 0.00 39.88 3.08
134 135 1.603326 GACTAGAGCGGTGCTACCTAC 59.397 57.143 0.00 0.00 39.88 3.18
135 136 1.212441 ACTAGAGCGGTGCTACCTACT 59.788 52.381 0.00 1.87 39.88 2.57
136 137 1.604755 CTAGAGCGGTGCTACCTACTG 59.395 57.143 0.00 0.00 39.88 2.74
138 139 2.202892 GCGGTGCTACCTACTGCC 60.203 66.667 0.00 0.00 43.05 4.85
139 140 3.014085 GCGGTGCTACCTACTGCCA 62.014 63.158 0.00 0.00 43.05 4.92
140 141 1.823295 CGGTGCTACCTACTGCCAT 59.177 57.895 4.21 0.00 35.66 4.40
141 142 0.249489 CGGTGCTACCTACTGCCATC 60.249 60.000 4.21 0.00 35.66 3.51
142 143 0.249489 GGTGCTACCTACTGCCATCG 60.249 60.000 0.00 0.00 34.73 3.84
143 144 0.460311 GTGCTACCTACTGCCATCGT 59.540 55.000 0.00 0.00 0.00 3.73
144 145 1.134788 GTGCTACCTACTGCCATCGTT 60.135 52.381 0.00 0.00 0.00 3.85
145 146 2.100252 GTGCTACCTACTGCCATCGTTA 59.900 50.000 0.00 0.00 0.00 3.18
146 147 2.361119 TGCTACCTACTGCCATCGTTAG 59.639 50.000 0.00 0.00 0.00 2.34
147 148 2.862921 GCTACCTACTGCCATCGTTAGC 60.863 54.545 0.00 0.00 0.00 3.09
148 149 1.486211 ACCTACTGCCATCGTTAGCT 58.514 50.000 0.00 0.00 0.00 3.32
149 150 1.409427 ACCTACTGCCATCGTTAGCTC 59.591 52.381 0.00 0.00 0.00 4.09
150 151 1.683917 CCTACTGCCATCGTTAGCTCT 59.316 52.381 0.00 0.00 0.00 4.09
151 152 2.287909 CCTACTGCCATCGTTAGCTCTC 60.288 54.545 0.00 0.00 0.00 3.20
152 153 1.479709 ACTGCCATCGTTAGCTCTCT 58.520 50.000 0.00 0.00 0.00 3.10
153 154 1.827969 ACTGCCATCGTTAGCTCTCTT 59.172 47.619 0.00 0.00 0.00 2.85
154 155 2.159170 ACTGCCATCGTTAGCTCTCTTC 60.159 50.000 0.00 0.00 0.00 2.87
155 156 1.137086 TGCCATCGTTAGCTCTCTTCC 59.863 52.381 0.00 0.00 0.00 3.46
156 157 1.137086 GCCATCGTTAGCTCTCTTCCA 59.863 52.381 0.00 0.00 0.00 3.53
157 158 2.801342 GCCATCGTTAGCTCTCTTCCAG 60.801 54.545 0.00 0.00 0.00 3.86
158 159 2.428890 CCATCGTTAGCTCTCTTCCAGT 59.571 50.000 0.00 0.00 0.00 4.00
159 160 3.443037 CATCGTTAGCTCTCTTCCAGTG 58.557 50.000 0.00 0.00 0.00 3.66
160 161 1.202582 TCGTTAGCTCTCTTCCAGTGC 59.797 52.381 0.00 0.00 41.26 4.40
161 162 1.634702 GTTAGCTCTCTTCCAGTGCG 58.365 55.000 0.00 0.00 44.91 5.34
162 163 0.532573 TTAGCTCTCTTCCAGTGCGG 59.467 55.000 0.00 0.00 44.91 5.69
163 164 1.323271 TAGCTCTCTTCCAGTGCGGG 61.323 60.000 0.00 0.00 44.91 6.13
164 165 2.650116 GCTCTCTTCCAGTGCGGGA 61.650 63.158 0.00 0.00 32.10 5.14
165 166 1.965754 GCTCTCTTCCAGTGCGGGAT 61.966 60.000 0.00 0.00 36.67 3.85
166 167 0.103937 CTCTCTTCCAGTGCGGGATC 59.896 60.000 0.00 0.00 36.67 3.36
167 168 0.324738 TCTCTTCCAGTGCGGGATCT 60.325 55.000 0.00 0.00 36.67 2.75
168 169 0.179089 CTCTTCCAGTGCGGGATCTG 60.179 60.000 0.00 0.00 36.67 2.90
169 170 0.904865 TCTTCCAGTGCGGGATCTGT 60.905 55.000 0.00 0.00 36.67 3.41
170 171 0.036010 CTTCCAGTGCGGGATCTGTT 60.036 55.000 0.00 0.00 36.67 3.16
171 172 0.400213 TTCCAGTGCGGGATCTGTTT 59.600 50.000 0.00 0.00 36.67 2.83
172 173 0.400213 TCCAGTGCGGGATCTGTTTT 59.600 50.000 0.00 0.00 34.36 2.43
173 174 1.202879 TCCAGTGCGGGATCTGTTTTT 60.203 47.619 0.00 0.00 34.36 1.94
174 175 1.200020 CCAGTGCGGGATCTGTTTTTC 59.800 52.381 0.00 0.00 0.00 2.29
217 218 0.035056 CCCGGAATCAAAGCTGTCCT 60.035 55.000 0.73 0.00 0.00 3.85
219 220 0.449388 CGGAATCAAAGCTGTCCTGC 59.551 55.000 0.00 0.00 0.00 4.85
223 224 3.243839 GGAATCAAAGCTGTCCTGCAAAA 60.244 43.478 0.00 0.00 34.99 2.44
257 258 2.508716 AGAGTCAAGATGCATCCACCAT 59.491 45.455 23.06 7.04 0.00 3.55
267 268 3.163467 TGCATCCACCATGTTTCATTCA 58.837 40.909 0.00 0.00 34.56 2.57
278 279 5.394443 CCATGTTTCATTCACCATTACCAGG 60.394 44.000 0.00 0.00 0.00 4.45
295 296 0.258774 AGGCACCAAGTTCCAACTGT 59.741 50.000 0.00 0.00 39.66 3.55
341 343 6.119144 TCCAACTGAAAAAGAAAGTTCTCG 57.881 37.500 0.00 0.00 36.28 4.04
343 345 6.150474 TCCAACTGAAAAAGAAAGTTCTCGTT 59.850 34.615 0.00 0.00 36.28 3.85
361 363 2.217620 CGTTGTGATTTTTCGGTTTGGC 59.782 45.455 0.00 0.00 0.00 4.52
381 383 1.138859 CAGGCCCATTCGACACATCTA 59.861 52.381 0.00 0.00 0.00 1.98
594 1068 4.825085 GGTGTTTCATTTCCTCCTTGTACA 59.175 41.667 0.00 0.00 0.00 2.90
639 1113 5.330233 TCTTCATCTACAACACTCCTACCA 58.670 41.667 0.00 0.00 0.00 3.25
658 1132 2.480419 CCAAACTTTGTCTGGAGTAGCG 59.520 50.000 0.88 0.00 31.38 4.26
749 1226 0.584876 CCGACACGGTTTTCTTCACC 59.415 55.000 1.80 0.00 42.73 4.02
768 1250 3.081804 ACCAGTATGCGAAGGGAAAAAG 58.918 45.455 0.00 0.00 31.97 2.27
770 1252 3.756434 CCAGTATGCGAAGGGAAAAAGAA 59.244 43.478 0.00 0.00 31.97 2.52
771 1253 4.142600 CCAGTATGCGAAGGGAAAAAGAAG 60.143 45.833 0.00 0.00 31.97 2.85
772 1254 4.455877 CAGTATGCGAAGGGAAAAAGAAGT 59.544 41.667 0.00 0.00 0.00 3.01
774 1256 1.953686 TGCGAAGGGAAAAAGAAGTGG 59.046 47.619 0.00 0.00 0.00 4.00
775 1257 1.954382 GCGAAGGGAAAAAGAAGTGGT 59.046 47.619 0.00 0.00 0.00 4.16
776 1258 2.287608 GCGAAGGGAAAAAGAAGTGGTG 60.288 50.000 0.00 0.00 0.00 4.17
777 1259 2.293399 CGAAGGGAAAAAGAAGTGGTGG 59.707 50.000 0.00 0.00 0.00 4.61
778 1260 3.562182 GAAGGGAAAAAGAAGTGGTGGA 58.438 45.455 0.00 0.00 0.00 4.02
779 1261 3.680777 AGGGAAAAAGAAGTGGTGGAA 57.319 42.857 0.00 0.00 0.00 3.53
780 1262 3.989056 AGGGAAAAAGAAGTGGTGGAAA 58.011 40.909 0.00 0.00 0.00 3.13
888 1370 5.510520 GCCACCAATTCTCCAATACAAAACA 60.511 40.000 0.00 0.00 0.00 2.83
890 1372 6.423604 CCACCAATTCTCCAATACAAAACAAC 59.576 38.462 0.00 0.00 0.00 3.32
895 1377 6.739331 TTCTCCAATACAAAACAACCCATT 57.261 33.333 0.00 0.00 0.00 3.16
920 1405 0.104855 TTCCATTCGCATCCTCCTCG 59.895 55.000 0.00 0.00 0.00 4.63
979 1464 1.760029 AGGAAGAAAGAGATCTCGCCC 59.240 52.381 16.97 12.09 34.09 6.13
1581 2066 3.376935 CTTCCGCGTGCCTGAGGAT 62.377 63.158 0.65 0.00 37.68 3.24
1633 2118 3.627952 TAGGAAACGGCGCCACCA 61.628 61.111 28.98 11.19 39.03 4.17
1728 2213 2.946329 TCTCTGATCTGCTACTCGGAAC 59.054 50.000 0.00 0.00 32.98 3.62
1743 2228 4.098960 ACTCGGAACAGACAAGTAAAGTCA 59.901 41.667 0.00 0.00 38.46 3.41
1765 2250 3.049912 GTGGCTGGTTGATTCGTTTTTC 58.950 45.455 0.00 0.00 0.00 2.29
1792 2277 9.241317 CAGAAACGAAGTACTTCTACTTGTTTA 57.759 33.333 28.30 0.00 45.00 2.01
1820 2305 3.847542 TCATACTACGCGTTGCCTTTAA 58.152 40.909 20.78 0.00 0.00 1.52
1823 2308 2.758009 ACTACGCGTTGCCTTTAAGAA 58.242 42.857 20.78 0.00 0.00 2.52
1886 2374 9.817809 ATACTACACACAGGATATACACAAAAG 57.182 33.333 0.00 0.00 0.00 2.27
2007 2495 5.109903 GTCTTGGTGTTACTAGCATACAGG 58.890 45.833 0.00 0.00 0.00 4.00
2036 2524 3.334583 AATTGCTGCTCCTCGTCTTAA 57.665 42.857 0.00 0.00 0.00 1.85
2040 2528 2.758423 TGCTGCTCCTCGTCTTAACATA 59.242 45.455 0.00 0.00 0.00 2.29
2041 2529 3.194755 TGCTGCTCCTCGTCTTAACATAA 59.805 43.478 0.00 0.00 0.00 1.90
2099 2587 7.099120 TCTTTTCAAGAGATCGATCAATGTGA 58.901 34.615 26.47 19.15 32.71 3.58
2104 2592 6.199719 TCAAGAGATCGATCAATGTGATTTCG 59.800 38.462 26.47 2.00 37.20 3.46
2205 2710 6.814506 ATGCTAATGTATCTTGCATCCTTC 57.185 37.500 0.00 0.00 39.79 3.46
2231 2736 4.082733 GGAGTGCCCTGTTTATTCTTTGAC 60.083 45.833 0.00 0.00 0.00 3.18
2263 2768 8.364142 AGCTGGATATCATTTGTAAGTCTAGTC 58.636 37.037 4.83 0.00 0.00 2.59
2267 2772 8.569641 GGATATCATTTGTAAGTCTAGTCTCGT 58.430 37.037 4.83 0.00 0.00 4.18
2326 2906 9.882996 GATCGAATTGCAATGACAGATAAATAA 57.117 29.630 13.82 0.00 0.00 1.40
2335 2915 8.128582 GCAATGACAGATAAATAACGGAAATGA 58.871 33.333 0.00 0.00 0.00 2.57
2425 3037 3.378112 CGTTATCATCAGGTTGCCATGTT 59.622 43.478 0.00 0.00 0.00 2.71
2516 3128 2.950781 TCCTCTCACTCTCCGCATTAT 58.049 47.619 0.00 0.00 0.00 1.28
2531 3143 0.846693 ATTATGTGCCACCCTCCTCC 59.153 55.000 0.00 0.00 0.00 4.30
2533 3145 2.194951 TATGTGCCACCCTCCTCCCT 62.195 60.000 0.00 0.00 0.00 4.20
2536 3148 3.412408 GCCACCCTCCTCCCTTCC 61.412 72.222 0.00 0.00 0.00 3.46
2537 3149 2.456840 CCACCCTCCTCCCTTCCT 59.543 66.667 0.00 0.00 0.00 3.36
2538 3150 1.690985 CCACCCTCCTCCCTTCCTC 60.691 68.421 0.00 0.00 0.00 3.71
2539 3151 1.394151 CACCCTCCTCCCTTCCTCT 59.606 63.158 0.00 0.00 0.00 3.69
2540 3152 0.252927 CACCCTCCTCCCTTCCTCTT 60.253 60.000 0.00 0.00 0.00 2.85
2541 3153 0.252927 ACCCTCCTCCCTTCCTCTTG 60.253 60.000 0.00 0.00 0.00 3.02
2542 3154 0.043334 CCCTCCTCCCTTCCTCTTGA 59.957 60.000 0.00 0.00 0.00 3.02
2543 3155 1.199615 CCTCCTCCCTTCCTCTTGAC 58.800 60.000 0.00 0.00 0.00 3.18
2544 3156 1.273552 CCTCCTCCCTTCCTCTTGACT 60.274 57.143 0.00 0.00 0.00 3.41
2545 3157 2.545810 CTCCTCCCTTCCTCTTGACTT 58.454 52.381 0.00 0.00 0.00 3.01
2546 3158 2.499693 CTCCTCCCTTCCTCTTGACTTC 59.500 54.545 0.00 0.00 0.00 3.01
2547 3159 2.158158 TCCTCCCTTCCTCTTGACTTCA 60.158 50.000 0.00 0.00 0.00 3.02
2548 3160 2.027653 CCTCCCTTCCTCTTGACTTCAC 60.028 54.545 0.00 0.00 0.00 3.18
2549 3161 2.903135 CTCCCTTCCTCTTGACTTCACT 59.097 50.000 0.00 0.00 0.00 3.41
2550 3162 2.900546 TCCCTTCCTCTTGACTTCACTC 59.099 50.000 0.00 0.00 0.00 3.51
2551 3163 2.903135 CCCTTCCTCTTGACTTCACTCT 59.097 50.000 0.00 0.00 0.00 3.24
2552 3164 3.056179 CCCTTCCTCTTGACTTCACTCTC 60.056 52.174 0.00 0.00 0.00 3.20
2553 3165 3.056179 CCTTCCTCTTGACTTCACTCTCC 60.056 52.174 0.00 0.00 0.00 3.71
2554 3166 3.534357 TCCTCTTGACTTCACTCTCCT 57.466 47.619 0.00 0.00 0.00 3.69
2555 3167 3.850752 TCCTCTTGACTTCACTCTCCTT 58.149 45.455 0.00 0.00 0.00 3.36
2556 3168 4.227197 TCCTCTTGACTTCACTCTCCTTT 58.773 43.478 0.00 0.00 0.00 3.11
2557 3169 4.039730 TCCTCTTGACTTCACTCTCCTTTG 59.960 45.833 0.00 0.00 0.00 2.77
2558 3170 3.733337 TCTTGACTTCACTCTCCTTTGC 58.267 45.455 0.00 0.00 0.00 3.68
2559 3171 2.154854 TGACTTCACTCTCCTTTGCG 57.845 50.000 0.00 0.00 0.00 4.85
2560 3172 1.686587 TGACTTCACTCTCCTTTGCGA 59.313 47.619 0.00 0.00 0.00 5.10
2561 3173 2.062519 GACTTCACTCTCCTTTGCGAC 58.937 52.381 0.00 0.00 0.00 5.19
2562 3174 1.412710 ACTTCACTCTCCTTTGCGACA 59.587 47.619 0.00 0.00 0.00 4.35
2563 3175 2.158957 ACTTCACTCTCCTTTGCGACAA 60.159 45.455 0.00 0.00 0.00 3.18
2564 3176 1.865865 TCACTCTCCTTTGCGACAAC 58.134 50.000 0.00 0.00 0.00 3.32
2565 3177 0.508641 CACTCTCCTTTGCGACAACG 59.491 55.000 0.00 0.00 42.93 4.10
2566 3178 0.600255 ACTCTCCTTTGCGACAACGG 60.600 55.000 8.23 8.23 40.15 4.44
2567 3179 0.600255 CTCTCCTTTGCGACAACGGT 60.600 55.000 12.43 0.00 40.15 4.83
2568 3180 0.179067 TCTCCTTTGCGACAACGGTT 60.179 50.000 12.43 0.00 40.15 4.44
2569 3181 0.234884 CTCCTTTGCGACAACGGTTC 59.765 55.000 12.43 0.00 40.15 3.62
2570 3182 1.083015 CCTTTGCGACAACGGTTCG 60.083 57.895 6.86 0.00 40.15 3.95
2571 3183 1.492319 CCTTTGCGACAACGGTTCGA 61.492 55.000 6.42 0.00 40.15 3.71
2572 3184 0.111266 CTTTGCGACAACGGTTCGAG 60.111 55.000 6.42 0.00 40.15 4.04
2573 3185 1.492319 TTTGCGACAACGGTTCGAGG 61.492 55.000 6.42 0.00 40.15 4.63
2574 3186 2.355481 GCGACAACGGTTCGAGGT 60.355 61.111 6.42 0.00 40.15 3.85
2575 3187 2.654912 GCGACAACGGTTCGAGGTG 61.655 63.158 6.42 0.00 40.15 4.00
2576 3188 2.019951 CGACAACGGTTCGAGGTGG 61.020 63.158 0.00 0.00 35.72 4.61
2577 3189 1.068585 GACAACGGTTCGAGGTGGT 59.931 57.895 0.00 0.00 0.00 4.16
2578 3190 0.531311 GACAACGGTTCGAGGTGGTT 60.531 55.000 0.00 0.00 0.00 3.67
2579 3191 0.812412 ACAACGGTTCGAGGTGGTTG 60.812 55.000 14.90 14.90 42.63 3.77
2580 3192 1.890510 AACGGTTCGAGGTGGTTGC 60.891 57.895 0.00 0.00 0.00 4.17
2581 3193 3.047877 CGGTTCGAGGTGGTTGCC 61.048 66.667 0.00 0.00 0.00 4.52
2582 3194 3.047877 GGTTCGAGGTGGTTGCCG 61.048 66.667 0.00 0.00 0.00 5.69
2583 3195 2.029964 GTTCGAGGTGGTTGCCGA 59.970 61.111 0.00 0.00 0.00 5.54
2584 3196 1.375523 GTTCGAGGTGGTTGCCGAT 60.376 57.895 0.00 0.00 0.00 4.18
2585 3197 0.953960 GTTCGAGGTGGTTGCCGATT 60.954 55.000 0.00 0.00 0.00 3.34
2586 3198 0.672401 TTCGAGGTGGTTGCCGATTC 60.672 55.000 0.00 0.00 0.00 2.52
2587 3199 2.106683 CGAGGTGGTTGCCGATTCC 61.107 63.158 0.00 0.00 0.00 3.01
2588 3200 1.299976 GAGGTGGTTGCCGATTCCT 59.700 57.895 0.00 0.00 0.00 3.36
2589 3201 0.744771 GAGGTGGTTGCCGATTCCTC 60.745 60.000 0.00 0.00 35.45 3.71
2590 3202 1.002624 GGTGGTTGCCGATTCCTCA 60.003 57.895 0.00 0.00 0.00 3.86
2591 3203 1.305930 GGTGGTTGCCGATTCCTCAC 61.306 60.000 0.00 0.00 0.00 3.51
2592 3204 1.002624 TGGTTGCCGATTCCTCACC 60.003 57.895 0.00 0.00 0.00 4.02
2593 3205 1.002624 GGTTGCCGATTCCTCACCA 60.003 57.895 0.00 0.00 0.00 4.17
2594 3206 0.394352 GGTTGCCGATTCCTCACCAT 60.394 55.000 0.00 0.00 0.00 3.55
2595 3207 1.017387 GTTGCCGATTCCTCACCATC 58.983 55.000 0.00 0.00 0.00 3.51
2596 3208 0.461870 TTGCCGATTCCTCACCATCG 60.462 55.000 0.00 0.00 41.65 3.84
2597 3209 1.326951 TGCCGATTCCTCACCATCGA 61.327 55.000 3.18 0.00 44.18 3.59
2598 3210 0.179084 GCCGATTCCTCACCATCGAA 60.179 55.000 3.18 0.00 44.18 3.71
2599 3211 1.541233 GCCGATTCCTCACCATCGAAT 60.541 52.381 3.18 0.00 44.18 3.34
2600 3212 2.408050 CCGATTCCTCACCATCGAATC 58.592 52.381 3.18 0.00 44.18 2.52
2602 3214 3.371102 GATTCCTCACCATCGAATCGA 57.629 47.619 8.12 8.12 41.13 3.59
2603 3215 2.871182 TTCCTCACCATCGAATCGAG 57.129 50.000 12.00 0.52 39.91 4.04
2604 3216 0.385751 TCCTCACCATCGAATCGAGC 59.614 55.000 12.00 0.00 39.91 5.03
2605 3217 0.936764 CCTCACCATCGAATCGAGCG 60.937 60.000 12.00 5.87 39.91 5.03
2606 3218 1.543941 CTCACCATCGAATCGAGCGC 61.544 60.000 12.00 0.00 39.91 5.92
2607 3219 2.279517 ACCATCGAATCGAGCGCC 60.280 61.111 12.00 0.00 39.91 6.53
2608 3220 3.398134 CCATCGAATCGAGCGCCG 61.398 66.667 12.00 8.02 39.91 6.46
2609 3221 2.655364 CATCGAATCGAGCGCCGT 60.655 61.111 12.00 0.00 39.91 5.68
2610 3222 2.104331 ATCGAATCGAGCGCCGTT 59.896 55.556 12.00 10.58 39.91 4.44
2611 3223 2.230940 ATCGAATCGAGCGCCGTTG 61.231 57.895 12.00 0.00 39.91 4.10
2612 3224 3.913573 CGAATCGAGCGCCGTTGG 61.914 66.667 16.00 8.77 39.75 3.77
2613 3225 2.813908 GAATCGAGCGCCGTTGGT 60.814 61.111 16.00 0.00 39.75 3.67
2614 3226 2.358247 AATCGAGCGCCGTTGGTT 60.358 55.556 16.00 0.00 39.75 3.67
2615 3227 2.563086 GAATCGAGCGCCGTTGGTTG 62.563 60.000 16.00 0.00 39.75 3.77
2618 3230 2.740826 GAGCGCCGTTGGTTGCTA 60.741 61.111 2.29 0.00 36.86 3.49
2619 3231 3.023591 GAGCGCCGTTGGTTGCTAC 62.024 63.158 2.29 0.00 36.86 3.58
2620 3232 4.097863 GCGCCGTTGGTTGCTACC 62.098 66.667 10.70 10.70 45.26 3.18
2629 3241 2.457080 GGTTGCTACCGTTGAGAGC 58.543 57.895 0.36 0.00 34.01 4.09
2630 3242 1.019805 GGTTGCTACCGTTGAGAGCC 61.020 60.000 0.36 0.00 35.24 4.70
2631 3243 1.080093 TTGCTACCGTTGAGAGCCG 60.080 57.895 0.00 0.00 35.24 5.52
2632 3244 2.886124 GCTACCGTTGAGAGCCGC 60.886 66.667 0.00 0.00 0.00 6.53
2633 3245 2.885861 CTACCGTTGAGAGCCGCT 59.114 61.111 0.00 0.00 0.00 5.52
2634 3246 1.226717 CTACCGTTGAGAGCCGCTC 60.227 63.158 12.80 12.80 44.21 5.03
2635 3247 2.615262 CTACCGTTGAGAGCCGCTCC 62.615 65.000 16.99 9.08 43.26 4.70
2636 3248 4.821589 CCGTTGAGAGCCGCTCCC 62.822 72.222 16.99 5.78 43.26 4.30
2637 3249 4.821589 CGTTGAGAGCCGCTCCCC 62.822 72.222 16.99 9.79 43.26 4.81
2638 3250 3.394836 GTTGAGAGCCGCTCCCCT 61.395 66.667 16.99 0.00 43.26 4.79
2639 3251 3.077556 TTGAGAGCCGCTCCCCTC 61.078 66.667 16.99 8.80 43.26 4.30
2680 3292 8.447787 TTTTTGCGAATCAAGAGCTTTATAAC 57.552 30.769 0.00 0.00 35.84 1.89
2681 3293 6.985188 TTGCGAATCAAGAGCTTTATAACT 57.015 33.333 0.00 0.00 0.00 2.24
2682 3294 6.589830 TGCGAATCAAGAGCTTTATAACTC 57.410 37.500 0.00 0.00 0.00 3.01
2683 3295 6.106003 TGCGAATCAAGAGCTTTATAACTCA 58.894 36.000 6.03 0.00 35.28 3.41
2684 3296 6.593770 TGCGAATCAAGAGCTTTATAACTCAA 59.406 34.615 6.03 0.00 35.28 3.02
2685 3297 7.280876 TGCGAATCAAGAGCTTTATAACTCAAT 59.719 33.333 6.03 0.00 35.28 2.57
2686 3298 8.125448 GCGAATCAAGAGCTTTATAACTCAATT 58.875 33.333 6.03 3.44 35.28 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.717313 GACCCCGGTGGCCACTTC 62.717 72.222 33.91 18.32 37.83 3.01
22 23 1.429148 GCACCGATGGTCATTCCGAC 61.429 60.000 0.00 0.00 44.57 4.79
23 24 1.153449 GCACCGATGGTCATTCCGA 60.153 57.895 0.00 0.00 39.52 4.55
24 25 1.431488 CTGCACCGATGGTCATTCCG 61.431 60.000 0.00 0.00 39.52 4.30
25 26 1.718757 GCTGCACCGATGGTCATTCC 61.719 60.000 0.00 0.00 31.02 3.01
26 27 1.723870 GCTGCACCGATGGTCATTC 59.276 57.895 0.00 0.00 31.02 2.67
27 28 2.108514 CGCTGCACCGATGGTCATT 61.109 57.895 0.00 0.00 31.02 2.57
28 29 2.512286 CGCTGCACCGATGGTCAT 60.512 61.111 0.00 0.00 31.02 3.06
29 30 3.647649 CTCGCTGCACCGATGGTCA 62.648 63.158 4.28 0.00 36.54 4.02
30 31 2.887568 CTCGCTGCACCGATGGTC 60.888 66.667 4.28 0.00 36.54 4.02
31 32 4.457496 CCTCGCTGCACCGATGGT 62.457 66.667 4.28 0.00 36.54 3.55
69 70 2.920912 TCCCGTCGAAGGCCACTT 60.921 61.111 12.40 0.00 40.34 3.16
70 71 3.382832 CTCCCGTCGAAGGCCACT 61.383 66.667 12.40 0.00 0.00 4.00
71 72 3.358076 CTCTCCCGTCGAAGGCCAC 62.358 68.421 12.40 0.00 0.00 5.01
72 73 3.068691 CTCTCCCGTCGAAGGCCA 61.069 66.667 12.40 0.00 0.00 5.36
73 74 4.516195 GCTCTCCCGTCGAAGGCC 62.516 72.222 12.40 0.00 0.00 5.19
74 75 4.856607 CGCTCTCCCGTCGAAGGC 62.857 72.222 12.40 0.00 0.00 4.35
75 76 4.194720 CCGCTCTCCCGTCGAAGG 62.195 72.222 10.80 10.80 0.00 3.46
76 77 4.194720 CCCGCTCTCCCGTCGAAG 62.195 72.222 0.00 0.00 0.00 3.79
95 96 3.524986 TAGCCTAGCCTAGCCCCCG 62.525 68.421 0.00 0.00 0.00 5.73
96 97 1.610967 CTAGCCTAGCCTAGCCCCC 60.611 68.421 0.00 0.00 0.00 5.40
97 98 0.901114 GTCTAGCCTAGCCTAGCCCC 60.901 65.000 2.79 0.00 35.78 5.80
98 99 0.113580 AGTCTAGCCTAGCCTAGCCC 59.886 60.000 2.79 0.00 35.78 5.19
99 100 2.306512 TCTAGTCTAGCCTAGCCTAGCC 59.693 54.545 11.17 0.00 35.78 3.93
100 101 3.606687 CTCTAGTCTAGCCTAGCCTAGC 58.393 54.545 11.17 0.00 35.78 3.42
101 102 3.606687 GCTCTAGTCTAGCCTAGCCTAG 58.393 54.545 9.99 9.99 35.43 3.02
102 103 2.027929 CGCTCTAGTCTAGCCTAGCCTA 60.028 54.545 2.82 0.00 36.60 3.93
103 104 1.271163 CGCTCTAGTCTAGCCTAGCCT 60.271 57.143 2.82 0.00 36.60 4.58
104 105 1.161843 CGCTCTAGTCTAGCCTAGCC 58.838 60.000 2.82 0.00 36.60 3.93
105 106 1.161843 CCGCTCTAGTCTAGCCTAGC 58.838 60.000 2.82 5.62 36.60 3.42
106 107 2.147958 CACCGCTCTAGTCTAGCCTAG 58.852 57.143 1.19 1.19 36.60 3.02
107 108 1.814634 GCACCGCTCTAGTCTAGCCTA 60.815 57.143 1.60 0.00 36.60 3.93
108 109 1.104577 GCACCGCTCTAGTCTAGCCT 61.105 60.000 1.60 0.00 36.60 4.58
109 110 1.104577 AGCACCGCTCTAGTCTAGCC 61.105 60.000 1.60 0.00 36.60 3.93
110 111 1.264826 GTAGCACCGCTCTAGTCTAGC 59.735 57.143 1.60 0.00 40.44 3.42
111 112 1.874872 GGTAGCACCGCTCTAGTCTAG 59.125 57.143 0.00 0.00 40.44 2.43
112 113 1.489649 AGGTAGCACCGCTCTAGTCTA 59.510 52.381 0.00 0.00 44.90 2.59
113 114 0.256464 AGGTAGCACCGCTCTAGTCT 59.744 55.000 0.00 0.00 44.90 3.24
114 115 1.603326 GTAGGTAGCACCGCTCTAGTC 59.397 57.143 0.00 0.00 44.90 2.59
115 116 1.212441 AGTAGGTAGCACCGCTCTAGT 59.788 52.381 0.00 0.00 44.90 2.57
116 117 1.604755 CAGTAGGTAGCACCGCTCTAG 59.395 57.143 0.00 0.00 44.90 2.43
117 118 1.676746 CAGTAGGTAGCACCGCTCTA 58.323 55.000 0.00 0.00 44.90 2.43
118 119 1.668101 GCAGTAGGTAGCACCGCTCT 61.668 60.000 0.00 0.00 44.90 4.09
119 120 1.227002 GCAGTAGGTAGCACCGCTC 60.227 63.158 0.00 0.00 44.90 5.03
120 121 2.722201 GGCAGTAGGTAGCACCGCT 61.722 63.158 0.00 0.00 44.90 5.52
121 122 2.202892 GGCAGTAGGTAGCACCGC 60.203 66.667 0.00 0.00 44.90 5.68
122 123 0.249489 GATGGCAGTAGGTAGCACCG 60.249 60.000 0.00 0.00 44.90 4.94
123 124 0.249489 CGATGGCAGTAGGTAGCACC 60.249 60.000 0.00 0.00 38.99 5.01
124 125 0.460311 ACGATGGCAGTAGGTAGCAC 59.540 55.000 0.00 0.00 0.00 4.40
125 126 1.191535 AACGATGGCAGTAGGTAGCA 58.808 50.000 0.00 0.00 0.00 3.49
126 127 2.862921 GCTAACGATGGCAGTAGGTAGC 60.863 54.545 16.87 16.87 32.44 3.58
127 128 2.623889 AGCTAACGATGGCAGTAGGTAG 59.376 50.000 3.47 7.18 35.08 3.18
128 129 2.621998 GAGCTAACGATGGCAGTAGGTA 59.378 50.000 3.47 0.00 35.08 3.08
129 130 1.409427 GAGCTAACGATGGCAGTAGGT 59.591 52.381 3.47 0.00 35.08 3.08
130 131 1.683917 AGAGCTAACGATGGCAGTAGG 59.316 52.381 3.47 0.00 35.08 3.18
131 132 2.621055 AGAGAGCTAACGATGGCAGTAG 59.379 50.000 3.47 0.00 35.08 2.57
132 133 2.656002 AGAGAGCTAACGATGGCAGTA 58.344 47.619 3.47 0.00 35.08 2.74
133 134 1.479709 AGAGAGCTAACGATGGCAGT 58.520 50.000 3.47 0.00 35.08 4.40
134 135 2.468831 GAAGAGAGCTAACGATGGCAG 58.531 52.381 3.47 0.00 35.08 4.85
135 136 1.137086 GGAAGAGAGCTAACGATGGCA 59.863 52.381 3.47 0.00 35.08 4.92
136 137 1.137086 TGGAAGAGAGCTAACGATGGC 59.863 52.381 0.00 0.00 0.00 4.40
137 138 2.428890 ACTGGAAGAGAGCTAACGATGG 59.571 50.000 0.00 0.00 37.43 3.51
138 139 3.443037 CACTGGAAGAGAGCTAACGATG 58.557 50.000 0.00 0.00 37.43 3.84
139 140 2.159170 GCACTGGAAGAGAGCTAACGAT 60.159 50.000 0.00 0.00 37.43 3.73
140 141 1.202582 GCACTGGAAGAGAGCTAACGA 59.797 52.381 0.00 0.00 37.43 3.85
141 142 1.634702 GCACTGGAAGAGAGCTAACG 58.365 55.000 0.00 0.00 37.43 3.18
142 143 1.634702 CGCACTGGAAGAGAGCTAAC 58.365 55.000 0.00 0.00 37.43 2.34
143 144 0.532573 CCGCACTGGAAGAGAGCTAA 59.467 55.000 0.00 0.00 42.00 3.09
144 145 1.323271 CCCGCACTGGAAGAGAGCTA 61.323 60.000 0.00 0.00 42.00 3.32
145 146 2.654079 CCCGCACTGGAAGAGAGCT 61.654 63.158 0.00 0.00 42.00 4.09
146 147 1.965754 ATCCCGCACTGGAAGAGAGC 61.966 60.000 0.00 0.00 42.00 4.09
147 148 0.103937 GATCCCGCACTGGAAGAGAG 59.896 60.000 0.00 0.00 42.00 3.20
148 149 0.324738 AGATCCCGCACTGGAAGAGA 60.325 55.000 0.00 0.00 42.00 3.10
149 150 0.179089 CAGATCCCGCACTGGAAGAG 60.179 60.000 0.00 0.00 42.00 2.85
150 151 0.904865 ACAGATCCCGCACTGGAAGA 60.905 55.000 0.00 0.00 42.00 2.87
151 152 0.036010 AACAGATCCCGCACTGGAAG 60.036 55.000 0.00 0.00 42.00 3.46
152 153 0.400213 AAACAGATCCCGCACTGGAA 59.600 50.000 0.00 0.00 42.00 3.53
153 154 0.400213 AAAACAGATCCCGCACTGGA 59.600 50.000 0.00 0.00 42.00 3.86
154 155 1.200020 GAAAAACAGATCCCGCACTGG 59.800 52.381 0.00 0.00 38.30 4.00
155 156 1.200020 GGAAAAACAGATCCCGCACTG 59.800 52.381 0.00 0.00 39.65 3.66
156 157 1.534729 GGAAAAACAGATCCCGCACT 58.465 50.000 0.00 0.00 0.00 4.40
157 158 0.526211 GGGAAAAACAGATCCCGCAC 59.474 55.000 0.00 0.00 45.56 5.34
158 159 2.955609 GGGAAAAACAGATCCCGCA 58.044 52.632 0.00 0.00 45.56 5.69
162 163 1.468914 GCACTCGGGAAAAACAGATCC 59.531 52.381 0.00 0.00 34.85 3.36
163 164 2.160417 CAGCACTCGGGAAAAACAGATC 59.840 50.000 0.00 0.00 0.00 2.75
164 165 2.154462 CAGCACTCGGGAAAAACAGAT 58.846 47.619 0.00 0.00 0.00 2.90
165 166 1.593196 CAGCACTCGGGAAAAACAGA 58.407 50.000 0.00 0.00 0.00 3.41
166 167 0.593128 CCAGCACTCGGGAAAAACAG 59.407 55.000 0.00 0.00 0.00 3.16
167 168 2.714259 CCAGCACTCGGGAAAAACA 58.286 52.632 0.00 0.00 0.00 2.83
174 175 2.825836 GCAATCCCAGCACTCGGG 60.826 66.667 0.00 0.00 46.03 5.14
189 190 1.281419 TTGATTCCGGGGTAGAAGCA 58.719 50.000 0.00 0.00 37.83 3.91
190 191 2.289565 CTTTGATTCCGGGGTAGAAGC 58.710 52.381 0.00 0.00 0.00 3.86
245 246 3.770388 TGAATGAAACATGGTGGATGCAT 59.230 39.130 0.00 0.00 35.15 3.96
246 247 3.056678 GTGAATGAAACATGGTGGATGCA 60.057 43.478 0.00 0.00 35.15 3.96
248 249 3.510753 TGGTGAATGAAACATGGTGGATG 59.489 43.478 0.00 0.00 38.15 3.51
249 250 3.777087 TGGTGAATGAAACATGGTGGAT 58.223 40.909 0.00 0.00 0.00 3.41
257 258 3.509575 GCCTGGTAATGGTGAATGAAACA 59.490 43.478 0.00 0.00 0.00 2.83
267 268 0.777446 ACTTGGTGCCTGGTAATGGT 59.223 50.000 0.00 0.00 0.00 3.55
278 279 4.278419 AGATTTACAGTTGGAACTTGGTGC 59.722 41.667 0.00 0.00 37.08 5.01
341 343 3.190874 TGCCAAACCGAAAAATCACAAC 58.809 40.909 0.00 0.00 0.00 3.32
343 345 2.223923 CCTGCCAAACCGAAAAATCACA 60.224 45.455 0.00 0.00 0.00 3.58
361 363 0.107508 AGATGTGTCGAATGGGCCTG 60.108 55.000 4.53 0.00 0.00 4.85
381 383 4.081198 TGCAAACATTTTGAAGAACCCACT 60.081 37.500 2.80 0.00 0.00 4.00
594 1068 2.097825 GCAATGTTGAGATCCAGCCTT 58.902 47.619 0.00 0.00 0.00 4.35
605 1079 6.430616 TGTTGTAGATGAAGATGCAATGTTGA 59.569 34.615 0.00 0.00 25.38 3.18
639 1113 2.143925 GCGCTACTCCAGACAAAGTTT 58.856 47.619 0.00 0.00 0.00 2.66
749 1226 4.455877 ACTTCTTTTTCCCTTCGCATACTG 59.544 41.667 0.00 0.00 0.00 2.74
801 1283 2.946752 GCGACGGGTCAACGGTTTC 61.947 63.158 0.00 0.00 38.39 2.78
835 1317 2.048597 TTAGCACCGACGCACCAG 60.049 61.111 0.00 0.00 0.00 4.00
888 1370 2.825532 CGAATGGAAGTGGAAATGGGTT 59.174 45.455 0.00 0.00 0.00 4.11
890 1372 1.134946 GCGAATGGAAGTGGAAATGGG 59.865 52.381 0.00 0.00 0.00 4.00
895 1377 1.281867 AGGATGCGAATGGAAGTGGAA 59.718 47.619 0.00 0.00 0.00 3.53
920 1405 1.312815 CGATTTGGATCTGGGGAAGC 58.687 55.000 0.00 0.00 0.00 3.86
1090 1575 2.514824 GGAGGCGATGGAGTTGGC 60.515 66.667 0.00 0.00 37.04 4.52
1092 1577 2.190578 GGGGAGGCGATGGAGTTG 59.809 66.667 0.00 0.00 0.00 3.16
1093 1578 3.470888 CGGGGAGGCGATGGAGTT 61.471 66.667 0.00 0.00 0.00 3.01
1137 1622 4.253257 GAGTCGTAGAGGCGGCCG 62.253 72.222 24.05 24.05 36.95 6.13
1227 1712 3.379445 GTGGCGTCGGAGAGGGAA 61.379 66.667 0.00 0.00 43.38 3.97
1633 2118 3.729108 TGATGAAGGAGAGGAGGTTGAT 58.271 45.455 0.00 0.00 0.00 2.57
1728 2213 3.496130 CAGCCACTGACTTTACTTGTCTG 59.504 47.826 0.00 0.00 38.67 3.51
1743 2228 1.981256 AAACGAATCAACCAGCCACT 58.019 45.000 0.00 0.00 0.00 4.00
1765 2250 6.214399 ACAAGTAGAAGTACTTCGTTTCTGG 58.786 40.000 25.92 20.65 44.81 3.86
1792 2277 4.684703 GGCAACGCGTAGTATGATCTTAAT 59.315 41.667 14.46 0.00 0.00 1.40
1820 2305 4.237976 TCTAATCTCCTCCTCACGTTCT 57.762 45.455 0.00 0.00 0.00 3.01
1823 2308 4.204012 CTCTTCTAATCTCCTCCTCACGT 58.796 47.826 0.00 0.00 0.00 4.49
1883 2371 4.852697 ACTAGATCCCAAGGTTCCTTCTTT 59.147 41.667 0.00 0.00 0.00 2.52
1886 2374 4.846168 AACTAGATCCCAAGGTTCCTTC 57.154 45.455 0.00 0.00 0.00 3.46
1988 2476 4.090819 TGTCCTGTATGCTAGTAACACCA 58.909 43.478 0.00 0.00 0.00 4.17
1990 2478 7.611213 ATTTTGTCCTGTATGCTAGTAACAC 57.389 36.000 0.00 0.00 0.00 3.32
2007 2495 4.795278 CGAGGAGCAGCAATTTATTTTGTC 59.205 41.667 0.00 0.00 0.00 3.18
2099 2587 6.349115 GCCAGAATCAAGATCATATGCGAAAT 60.349 38.462 0.00 0.00 0.00 2.17
2104 2592 3.750130 ACGCCAGAATCAAGATCATATGC 59.250 43.478 0.00 0.00 0.00 3.14
2179 2668 7.250032 AGGATGCAAGATACATTAGCATAGA 57.750 36.000 0.00 0.00 45.08 1.98
2205 2710 3.690460 AGAATAAACAGGGCACTCCAAG 58.310 45.455 0.00 0.00 38.24 3.61
2231 2736 7.230108 ACTTACAAATGATATCCAGCTCCAATG 59.770 37.037 0.00 0.00 0.00 2.82
2284 2789 8.706936 GCAATTCGATCGATGATAGCATTATAT 58.293 33.333 20.18 1.21 34.11 0.86
2292 2797 6.128742 TGTCATTGCAATTCGATCGATGATAG 60.129 38.462 20.18 8.71 34.31 2.08
2346 2926 8.778358 AGCTAAATATCATTTCCGTGAATTCTC 58.222 33.333 7.05 1.90 0.00 2.87
2353 2933 5.234329 ACGTCAGCTAAATATCATTTCCGTG 59.766 40.000 0.00 0.00 0.00 4.94
2405 2985 4.574421 CGTAACATGGCAACCTGATGATAA 59.426 41.667 0.00 0.00 35.94 1.75
2461 3073 0.032403 CGGTACAGGGTTCGTTCACA 59.968 55.000 0.00 0.00 0.00 3.58
2463 3075 1.667151 CCGGTACAGGGTTCGTTCA 59.333 57.895 3.79 0.00 0.00 3.18
2464 3076 1.739196 GCCGGTACAGGGTTCGTTC 60.739 63.158 14.25 0.00 0.00 3.95
2465 3077 2.344872 GCCGGTACAGGGTTCGTT 59.655 61.111 14.25 0.00 0.00 3.85
2466 3078 2.918802 TGCCGGTACAGGGTTCGT 60.919 61.111 14.25 0.00 0.00 3.85
2516 3128 3.810687 AAGGGAGGAGGGTGGCACA 62.811 63.158 20.82 0.00 0.00 4.57
2522 3134 0.252927 CAAGAGGAAGGGAGGAGGGT 60.253 60.000 0.00 0.00 0.00 4.34
2526 3138 2.158158 TGAAGTCAAGAGGAAGGGAGGA 60.158 50.000 0.00 0.00 0.00 3.71
2529 3141 2.900546 GAGTGAAGTCAAGAGGAAGGGA 59.099 50.000 0.00 0.00 0.00 4.20
2531 3143 3.056179 GGAGAGTGAAGTCAAGAGGAAGG 60.056 52.174 0.00 0.00 0.00 3.46
2533 3145 3.850752 AGGAGAGTGAAGTCAAGAGGAA 58.149 45.455 0.00 0.00 0.00 3.36
2536 3148 3.745458 GCAAAGGAGAGTGAAGTCAAGAG 59.255 47.826 0.00 0.00 0.00 2.85
2537 3149 3.733337 GCAAAGGAGAGTGAAGTCAAGA 58.267 45.455 0.00 0.00 0.00 3.02
2538 3150 2.478134 CGCAAAGGAGAGTGAAGTCAAG 59.522 50.000 0.00 0.00 0.00 3.02
2539 3151 2.102420 TCGCAAAGGAGAGTGAAGTCAA 59.898 45.455 0.00 0.00 0.00 3.18
2540 3152 1.686587 TCGCAAAGGAGAGTGAAGTCA 59.313 47.619 0.00 0.00 0.00 3.41
2541 3153 2.062519 GTCGCAAAGGAGAGTGAAGTC 58.937 52.381 0.00 0.00 0.00 3.01
2542 3154 1.412710 TGTCGCAAAGGAGAGTGAAGT 59.587 47.619 0.00 0.00 0.00 3.01
2543 3155 2.154854 TGTCGCAAAGGAGAGTGAAG 57.845 50.000 0.00 0.00 0.00 3.02
2544 3156 2.210116 GTTGTCGCAAAGGAGAGTGAA 58.790 47.619 0.00 0.00 0.00 3.18
2545 3157 1.865865 GTTGTCGCAAAGGAGAGTGA 58.134 50.000 0.00 0.00 0.00 3.41
2546 3158 0.508641 CGTTGTCGCAAAGGAGAGTG 59.491 55.000 0.00 0.00 0.00 3.51
2547 3159 0.600255 CCGTTGTCGCAAAGGAGAGT 60.600 55.000 15.55 0.00 35.54 3.24
2548 3160 0.600255 ACCGTTGTCGCAAAGGAGAG 60.600 55.000 23.26 5.32 35.54 3.20
2549 3161 0.179067 AACCGTTGTCGCAAAGGAGA 60.179 50.000 23.26 0.00 35.54 3.71
2550 3162 0.234884 GAACCGTTGTCGCAAAGGAG 59.765 55.000 23.26 6.11 35.54 3.69
2551 3163 1.492319 CGAACCGTTGTCGCAAAGGA 61.492 55.000 23.26 0.00 35.54 3.36
2552 3164 1.083015 CGAACCGTTGTCGCAAAGG 60.083 57.895 17.80 17.80 35.54 3.11
2553 3165 0.111266 CTCGAACCGTTGTCGCAAAG 60.111 55.000 0.00 0.00 35.54 2.77
2554 3166 1.492319 CCTCGAACCGTTGTCGCAAA 61.492 55.000 0.00 0.00 35.54 3.68
2555 3167 1.952133 CCTCGAACCGTTGTCGCAA 60.952 57.895 0.00 0.00 35.54 4.85
2556 3168 2.355363 CCTCGAACCGTTGTCGCA 60.355 61.111 0.00 0.00 35.54 5.10
2557 3169 2.355481 ACCTCGAACCGTTGTCGC 60.355 61.111 0.00 0.00 35.54 5.19
2558 3170 2.019951 CCACCTCGAACCGTTGTCG 61.020 63.158 0.00 0.00 0.00 4.35
2559 3171 0.531311 AACCACCTCGAACCGTTGTC 60.531 55.000 0.00 0.00 0.00 3.18
2560 3172 0.812412 CAACCACCTCGAACCGTTGT 60.812 55.000 0.00 0.00 31.36 3.32
2561 3173 1.938861 CAACCACCTCGAACCGTTG 59.061 57.895 0.00 0.00 0.00 4.10
2562 3174 1.890510 GCAACCACCTCGAACCGTT 60.891 57.895 0.00 0.00 0.00 4.44
2563 3175 2.280592 GCAACCACCTCGAACCGT 60.281 61.111 0.00 0.00 0.00 4.83
2564 3176 3.047877 GGCAACCACCTCGAACCG 61.048 66.667 0.00 0.00 0.00 4.44
2565 3177 2.798148 ATCGGCAACCACCTCGAACC 62.798 60.000 0.00 0.00 35.25 3.62
2566 3178 0.953960 AATCGGCAACCACCTCGAAC 60.954 55.000 0.00 0.00 35.25 3.95
2567 3179 0.672401 GAATCGGCAACCACCTCGAA 60.672 55.000 0.00 0.00 35.25 3.71
2568 3180 1.079405 GAATCGGCAACCACCTCGA 60.079 57.895 0.00 0.00 36.07 4.04
2569 3181 2.106683 GGAATCGGCAACCACCTCG 61.107 63.158 0.00 0.00 0.00 4.63
2570 3182 0.744771 GAGGAATCGGCAACCACCTC 60.745 60.000 0.00 0.00 37.37 3.85
2571 3183 1.299976 GAGGAATCGGCAACCACCT 59.700 57.895 0.00 0.00 0.00 4.00
2572 3184 1.002624 TGAGGAATCGGCAACCACC 60.003 57.895 0.00 0.00 0.00 4.61
2573 3185 1.305930 GGTGAGGAATCGGCAACCAC 61.306 60.000 0.00 0.00 0.00 4.16
2574 3186 1.002624 GGTGAGGAATCGGCAACCA 60.003 57.895 0.00 0.00 0.00 3.67
2575 3187 0.394352 ATGGTGAGGAATCGGCAACC 60.394 55.000 0.00 0.00 0.00 3.77
2576 3188 1.017387 GATGGTGAGGAATCGGCAAC 58.983 55.000 0.00 0.00 0.00 4.17
2577 3189 0.461870 CGATGGTGAGGAATCGGCAA 60.462 55.000 0.00 0.00 41.49 4.52
2578 3190 1.143838 CGATGGTGAGGAATCGGCA 59.856 57.895 0.00 0.00 41.49 5.69
2579 3191 0.179084 TTCGATGGTGAGGAATCGGC 60.179 55.000 5.34 0.00 44.48 5.54
2580 3192 2.408050 GATTCGATGGTGAGGAATCGG 58.592 52.381 5.34 0.00 44.48 4.18
2582 3194 3.312828 CTCGATTCGATGGTGAGGAATC 58.687 50.000 9.54 3.54 41.51 2.52
2583 3195 2.546795 GCTCGATTCGATGGTGAGGAAT 60.547 50.000 9.54 0.00 34.61 3.01
2584 3196 1.202417 GCTCGATTCGATGGTGAGGAA 60.202 52.381 9.54 0.00 34.61 3.36
2585 3197 0.385751 GCTCGATTCGATGGTGAGGA 59.614 55.000 9.54 0.00 34.61 3.71
2586 3198 0.936764 CGCTCGATTCGATGGTGAGG 60.937 60.000 9.54 0.00 34.61 3.86
2587 3199 1.543941 GCGCTCGATTCGATGGTGAG 61.544 60.000 9.54 1.00 34.61 3.51
2588 3200 1.588932 GCGCTCGATTCGATGGTGA 60.589 57.895 9.54 0.00 34.61 4.02
2589 3201 2.589492 GGCGCTCGATTCGATGGTG 61.589 63.158 9.54 6.85 34.61 4.17
2590 3202 2.279517 GGCGCTCGATTCGATGGT 60.280 61.111 9.54 0.00 34.61 3.55
2591 3203 3.398134 CGGCGCTCGATTCGATGG 61.398 66.667 9.54 5.74 42.43 3.51
2592 3204 2.230940 AACGGCGCTCGATTCGATG 61.231 57.895 22.10 6.65 42.43 3.84
2593 3205 2.104331 AACGGCGCTCGATTCGAT 59.896 55.556 22.10 2.01 42.43 3.59
2594 3206 2.878991 CAACGGCGCTCGATTCGA 60.879 61.111 22.10 8.70 42.43 3.71
2595 3207 3.913573 CCAACGGCGCTCGATTCG 61.914 66.667 22.10 12.08 42.43 3.34
2596 3208 2.388232 AACCAACGGCGCTCGATTC 61.388 57.895 22.10 0.00 42.43 2.52
2597 3209 2.358247 AACCAACGGCGCTCGATT 60.358 55.556 22.10 11.23 42.43 3.34
2598 3210 3.118454 CAACCAACGGCGCTCGAT 61.118 61.111 22.10 9.85 42.43 3.59
2601 3213 2.740826 TAGCAACCAACGGCGCTC 60.741 61.111 6.90 0.00 36.40 5.03
2602 3214 3.047877 GTAGCAACCAACGGCGCT 61.048 61.111 6.90 0.00 38.18 5.92
2603 3215 4.097863 GGTAGCAACCAACGGCGC 62.098 66.667 6.90 0.00 45.98 6.53
2611 3223 1.019805 GGCTCTCAACGGTAGCAACC 61.020 60.000 3.32 0.00 42.95 3.77
2612 3224 1.352156 CGGCTCTCAACGGTAGCAAC 61.352 60.000 3.32 0.00 38.01 4.17
2613 3225 1.080093 CGGCTCTCAACGGTAGCAA 60.080 57.895 3.32 0.00 38.01 3.91
2614 3226 2.571757 CGGCTCTCAACGGTAGCA 59.428 61.111 3.32 0.00 38.01 3.49
2615 3227 2.886124 GCGGCTCTCAACGGTAGC 60.886 66.667 0.00 0.00 35.47 3.58
2616 3228 1.226717 GAGCGGCTCTCAACGGTAG 60.227 63.158 22.32 0.00 41.25 3.18
2617 3229 2.707849 GGAGCGGCTCTCAACGGTA 61.708 63.158 27.47 0.00 43.70 4.02
2618 3230 4.070552 GGAGCGGCTCTCAACGGT 62.071 66.667 27.47 0.00 43.70 4.83
2619 3231 4.821589 GGGAGCGGCTCTCAACGG 62.822 72.222 27.47 0.00 43.70 4.44
2620 3232 4.821589 GGGGAGCGGCTCTCAACG 62.822 72.222 29.52 0.00 43.70 4.10
2621 3233 3.378399 GAGGGGAGCGGCTCTCAAC 62.378 68.421 29.52 18.71 43.70 3.18
2622 3234 3.077556 GAGGGGAGCGGCTCTCAA 61.078 66.667 29.52 0.00 43.70 3.02
2655 3267 8.296713 AGTTATAAAGCTCTTGATTCGCAAAAA 58.703 29.630 0.00 0.00 35.74 1.94
2656 3268 7.816640 AGTTATAAAGCTCTTGATTCGCAAAA 58.183 30.769 0.00 0.00 35.74 2.44
2657 3269 7.119116 TGAGTTATAAAGCTCTTGATTCGCAAA 59.881 33.333 0.00 0.00 35.74 3.68
2658 3270 6.593770 TGAGTTATAAAGCTCTTGATTCGCAA 59.406 34.615 0.00 0.00 33.22 4.85
2659 3271 6.106003 TGAGTTATAAAGCTCTTGATTCGCA 58.894 36.000 0.00 0.00 33.22 5.10
2660 3272 6.589830 TGAGTTATAAAGCTCTTGATTCGC 57.410 37.500 0.00 0.00 33.22 4.70


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.